September 2003 Commit Log

Number of Commits:

166

Number of Active Developers:

5

huberj 2003-09-30 17:04 #166 Rev.: 1966

*** empty log message ***

252 lines of code changed in 8 files:

• SEQ_QUALITY: Makefile (+3 -1), SQ_GroupData.cxx (new 48), SQ_GroupData.h (new 39), SQ_consensus.h (+44 -19), SQ_functions.cxx (+76 -66), SQ_functions.h (+6 -1), SQ_main.cxx (+16 -1), SQ_physical_layout.h (+20 -24)

westram 2003-09-29 09:51 #165 Rev.: 1965

- classes output/indent moved here

128 lines of code changed in 1 file:

• TEMPLATES: output.h (new 128)

westram 2003-09-29 09:50 #164 Rev.: 1964

- added output.h

1 lines of code changed in 1 file:

• SOURCE_TOOLS: generate_all_links.sh (+1)

westram 2003-09-29 09:50 #163 Rev.: 1963

- displays group names

10 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeNode.java (+10 -1)

westram 2003-09-29 09:49 #162 Rev.: 1962

- fixed encode for root node

3 lines of code changed in 1 file:

• PROBE_SERVER/WORKER: psw_main.cxx (+3 -2)

westram 2003-09-29 09:49 #161 Rev.: 1961

- inserts max coverage into tree
- changed CL interface

75 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP_DESIGN: pgd_main.cxx (+75 -33)

westram 2003-09-29 09:48 #160 Rev.: 1960

cosmetics

12 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP: pg_db.cxx (+12 -14)

westram 2003-09-29 09:47 #159 Rev.: 1959

- uses deque instead of set
- fixed memory leak

31 lines of code changed in 2 files:

• PROBE_SERVER/PROBE_GROUP: pg_search.cxx (+26 -17), pg_search.hxx (+5 -2)

westram 2003-09-29 09:46 #158 Rev.: 1958

- all inner nodes know their number of species
- now everything uses deque (instead of set)
- TreeTraversal owns a deque of SpeciesIDs and keeps it up to date
(avoids multiple recursion of subtrees)
- TreeTraversal traverses root-node (was skipped before)
- removed classes output and indent (now in TEMPLATES/output.h)
- propagates exact groups upwards as coverage groups

369 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP: pg_main.cxx (+369 -188)

westram 2003-09-29 09:45 #157 Rev.: 1957

- merges generated trees
- changed call to arb_probe_group_design

37 lines of code changed in 1 file:

• PROBE_SERVER: update_probe_server_databases.sh (+37 -13)

westram 2003-09-29 09:43 #156 Rev.: 1956

- added target 'pgd_tree_merge'

7 lines of code changed in 1 file:

• PROBE_SERVER: Makefile (+7)

westram 2003-09-29 09:43 #155 Rev.: 1955

- merges several trees saved by arb_probe_group_design

433 lines of code changed in 2 files:

• PROBE_SERVER/TREE_MERGE: Makefile (new 37), tree_merge.cxx (new 396)

huberj 2003-09-27 15:59 #154 Rev.: 1954

*** empty log message ***

389 lines of code changed in 8 files:

• SEQ_QUALITY: Makefile (+4 -6), SQ_ambiguities.h (+10 -2), SQ_consensus.h (new 91), SQ_consensus_marked.h (del), SQ_functions.cxx (+45 -114), SQ_helix.h (new 128), SQ_main.cxx (+1 -1), SQ_physical_layout.h (new 110)

westram 2003-09-26 17:05 #153 Rev.: 1953

*** empty log message ***

2 lines of code changed in 1 file:

• arb_INSTALL.txt (+2 -1)

westram 2003-09-26 17:02 #152 Rev.: 1952

- splitted spaghetti-main() into various functions

263 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP: pg_main.cxx (+263 -277)

westram 2003-09-26 15:07 #151 Rev.: 1951

- splitted spaghetti-main() into various functions

274 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP_DESIGN: pgd_main.cxx (+274 -247)

westram 2003-09-26 15:07 #150 Rev.: 1950

- echoes probe_group.. commands

2 lines of code changed in 1 file:

• PROBE_SERVER: update_probe_server_databases.sh (+2)

westram 2003-09-26 13:26 #149 Rev.: 1949

cosmetics

2 lines of code changed in 2 files:

• PROBE_WEB/CLIENT: ProbesGUI.java (-1), TreeParser.java (+2 -5)

westram 2003-09-26 13:25 #148 Rev.: 1948

- cleaned displayTreeGraph()
- vertical lines are drawn seperately for upper and lower part
to allow different colors and they belong to the child node
(not to the parent node).
- probe info is displayed in different color

106 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeDisplay.java (+106 -119)

westram 2003-09-26 13:24 #147 Rev.: 1947

- changed semantics of 'marked' flag
- automatically updates mark flags for parent nodes
- node information for inner nodes

79 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeNode.java (+79 -16)

westram 2003-09-26 13:22 #146 Rev.: 1946

- commented out unused stuff
- added toggle to show/hide unimplemented menus

54 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: ProbeMenu.java (+54 -47)

westram 2003-09-26 13:21 #145 Rev.: 1945

- fixed errors in decodePath and initDecodeTable
- more error messages (even for thing that never should occur)

56 lines of code changed in 1 file:

• PROBE_SERVER/WORKER: psw_main.cxx (+56 -41)

westram 2003-09-26 13:20 #144 Rev.: 1944

- writes back number of exact matches to subtree.
may have changed by searching common probes
- cleanup

29 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP_DESIGN: pgd_main.cxx (+29 -99)

westram 2003-09-26 13:19 #143 Rev.: 1943

- wrote wrong size to 'exact'

2 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP: pg_main.cxx (+2 -1)

westram 2003-09-26 13:19 #142 Rev.: 1942

- fixed misleading console output

4 lines of code changed in 1 file:

• PROBE_SERVER: update_probe_server_databases.sh (+4 -2)

westram 2003-09-26 09:37 #141 Rev.: 1941

- increased stack size to be able to handle up to 250.000 species
(has been 50.000)

2 lines of code changed in 1 file:

• PARSIMONY: AP_buffer.cxx (+2 -1)

westram 2003-09-25 17:02 #140 Rev.: 1940

*** empty log message ***

58 lines of code changed in 3 files:

• SEQ_QUALITY: Makefile (+3 -2), SQ_consensus_marked.h (+20 -18), SQ_functions.cxx (+35 -22)

huberj 2003-09-25 13:11 #139 Rev.: 1939

*** empty log message ***

8 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+8 -6)

westram 2003-09-25 10:23 #138 Rev.: 1938

- cosmetics

3 lines of code changed in 1 file:

• Makefile (+3 -4)

westram 2003-09-25 10:20 #137 Rev.: 1937

- added cache for probe groups
- fixes for changed db structure

193 lines of code changed in 1 file:

• PROBE_SERVER/WORKER: psw_main.cxx (+193 -59)

westram 2003-09-25 10:20 #136 Rev.: 1936

- made all functions static
- fixes for changed database structure

292 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP_DESIGN: pgd_main.cxx (+292 -92)

westram 2003-09-25 10:20 #135 Rev.: 1935

- generates ALL treenodes (even those w/o probes found)
- removed subtree/species, added subtree/member (leafs only)
- probes are collected in 'probe_groups/probe_group' containers
- skip zero occurances from statistic

95 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP: pg_main.cxx (+95 -65)

westram 2003-09-25 10:18 #134 Rev.: 1934

updated

2 lines of code changed in 1 file:

• arb_INSTALL.txt (+2 -2)

westram 2003-09-23 12:16 #133 Rev.: 1932

script to generate java dependencies

33 lines of code changed in 1 file:

• SOURCE_TOOLS: make_java_dependencies.sh (new 33)

westram 2003-09-23 09:55 #132 Rev.: 1931

minor changes

13 lines of code changed in 2 files:

• PROBE_WEB/CLIENT: TreeDisplay.java (+11 -19), TreeReader.java (+2 -2)

westram 2003-09-23 09:54 #131 Rev.: 1930

- removed naming of internal nodes ('anchor' and 'root')
- rewrote tree parser recursively
- decodes node info

534 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeParser.java (+534 -257)

westram 2003-09-23 09:53 #130 Rev.: 1929

- added data elements for information from tree + access functions
- added getNodeInformation() (string displayed for node)

85 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeNode.java (+85 -40)

westram 2003-09-23 09:53 #129 Rev.: 1928

changed user message

2 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: Toolkit.java (+2 -2)

westram 2003-09-23 09:53 #128 Rev.: 1927

- added parameters needResult and beNoisy

46 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: ServerAnswer.java (+46 -24)

westram 2003-09-23 09:52 #127 Rev.: 1926

- dumps changed TreeNode variables

13 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: NodeError.java (+13 -15)

westram 2003-09-23 09:51 #126 Rev.: 1925

- generates dependencies

12 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: Makefile (+12 -4)

westram 2003-09-23 09:51 #125 Rev.: 1924

- modified error message
- cleanup

13 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: HttpSubsystem.java (+13 -74)

westram 2003-09-23 09:51 #124 Rev.: 1923

superfluous newline

1 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: CommandLine.java (+1 -1)

westram 2003-09-23 09:50 #123 Rev.: 1922

*** empty log message ***

0 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: .depends (new)

westram 2003-09-23 09:50 #122 Rev.: 1921

- readTree allows to reload the tree

26 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: Client.java (+26 -20)

westram 2003-09-23 09:46 #121 Rev.: 1920

- 'depends' removes CLIENT/.depends

2 lines of code changed in 1 file:

• PROBE_WEB: Makefile (+2 -1)

westram 2003-09-23 09:45 #120 Rev.: 1919

- updated comment

2 lines of code changed in 1 file:

• PROBE_SERVER: common.h (+2 -1)

westram 2003-09-23 09:45 #119 Rev.: 1918

- updated description of tree format

59 lines of code changed in 1 file:

• PROBE_SERVER: treeformat.README (new 59)

westram 2003-09-23 09:45 #118 Rev.: 1917

- 'p=' -> 'em='

2 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP_DESIGN: pgd_main.cxx (+2 -2)

huberj 2003-09-22 17:04 #117 Rev.: 1916

*** empty log message ***

116 lines of code changed in 5 files:

• SEQ_QUALITY: SQ_ambiguities.h (+15), SQ_consensus_marked.h (+15), SQ_functions.cxx (+80 -22), SQ_functions.h (+5 -5), SQ_main.cxx (+1)

westram 2003-09-21 13:34 #116 Rev.: 1915

- uses getFiletime.pl

3 lines of code changed in 1 file:

• PROBE_SERVER: update_probe_server_databases.sh (+3 -2)

westram 2003-09-21 13:33 #115 Rev.: 1914

- replacement for 'stat' command

3 lines of code changed in 1 file:

• PROBE_SERVER: getFiletime.pl (new 3)

westram 2003-09-21 13:15 #114 Rev.: 1913

*** empty log message ***

1 lines of code changed in 1 file:

• PROBE_SET: .cvsignore (new 1)

westram 2003-09-21 13:14 #113 Rev.: 1912

jar name changed

1 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: .cvsignore (+1 -1)

westram 2003-09-21 13:14 #112 Rev.: 1911

dependencies updated

3 lines of code changed in 2 files:

• PROBE_SERVER/PROBE_GROUP: Makefile (+2 -2)
• SEQ_QUALITY: Makefile (+1)

westram 2003-09-21 13:13 #111 Rev.: 1910

- added clientfilename() and print_download_header()

11 lines of code changed in 1 file:

• PROBE_WEB/SERVER: probe_server.pm (+11 -3)

westram 2003-09-21 13:13 #110 Rev.: 1909

- this in fact is a perl script to download
the arb_probe_library client

16 lines of code changed in 1 file:

• PROBE_WEB/SERVER: arb_probe_library.jar (new 16)

westram 2003-09-21 13:11 #109 Rev.: 1908

- clicking into unknown area -> search leftwards for known area

3 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeDisplay.java (+3)

westram 2003-09-21 13:09 #108 Rev.: 1907

- does no longer generate c files
- only generates dependencies for SOURCES_TML

48 lines of code changed in 1 file:

• GDE/MOLPHY: Makefile (+48 -86)

westram 2003-09-21 12:53 #107 Rev.: 1906

- changed path encoding
- reads probes from different container

20 lines of code changed in 1 file:

• PROBE_SERVER/WORKER: psw_main.cxx (+20 -11)

westram 2003-09-21 12:53 #106 Rev.: 1905

- takes version number of treefile as argument
- calculated probes go into different container
- adds number of found probes to tree
- saves the tree
- wrote own tree export function

213 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP_DESIGN: pgd_main.cxx (+213 -15)

westram 2003-09-21 12:53 #105 Rev.: 1904

- strings written to tree nodes: converts kommas to underscores
- saves fullname and acc in tree

48 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP: pg_main.cxx (+48 -9)

westram 2003-09-21 12:52 #104 Rev.: 1903

- updates client zip
- generates treefile with correct date
- asks arb_probe_group_design to create tree

41 lines of code changed in 1 file:

• PROBE_SERVER: update_probe_server_databases.sh (+41 -1)

westram 2003-09-21 12:52 #103 Rev.: 1902

- encode/decode for tree nodes (escapes "_,;:'")

60 lines of code changed in 1 file:

• PROBE_SERVER: common.h (+60 -1)

huberj 2003-09-19 16:46 #102 Rev.: 1901

*** empty log message ***

149 lines of code changed in 6 files:

• NTREE: NT_extern.cxx (+1 -1)
• SEQ_QUALITY: SQ_ambiguities.h (new 97), SQ_functions.cxx (+37 -21), SQ_functions.h (+2 -2), SQ_main.cxx (+9 -2)
• lib/pictures: seq_quality.fig (+3 -1)

westram 2003-09-19 11:13 #101 Rev.: 1900

- automatically create bin dir

4 lines of code changed in 1 file:

• PROBE_SET: Makefile (+4 -1)

westram 2003-09-19 11:12 #100 Rev.: 1899

- const fix

9 lines of code changed in 1 file:

• CHIP: ca_mark.cxx (+9 -9)

westram 2003-09-19 11:00 #99 Rev.: 1898

*** empty log message ***

1 lines of code changed in 1 file:

• arb_CHANGES.txt (+1 -1)

westram 2003-09-19 10:58 #98 Rev.: 1897

- removes treefile
- tests for empty input file

40 lines of code changed in 1 file:

• SH: arb_protml (+40 -31)

westram 2003-09-19 10:37 #97 Rev.: 1896

- used wrong input filename for normal protml

1 lines of code changed in 1 file:

• GDEHELP/MENUS: molphy.menu (+1 -1)

westram 2003-09-19 10:34 #96 Rev.: 1895

- added flag to raise warnings

7 lines of code changed in 1 file:

• GDE: Makefile (+7)

westram 2003-09-19 10:33 #95 Rev.: 1894

const fix

19 lines of code changed in 3 files:

• GDE/TREEPUZZLE: ChangeLog (+3)
• GDE/TREEPUZZLE/src: util.c (+15 -15), util.h (+1 -1)

westram 2003-09-19 10:32 #94 Rev.: 1893

*** empty log message ***

0 lines of code changed in 1 file:

• GDE/MOLPHY: .cvsignore (new)

westram 2003-09-19 10:31 #93 Rev.: 1892

- missing parameter type
- one array element wasn't initialized

8 lines of code changed in 1 file:

• GDE/MOLPHY: sltree.c (+8 -9)

westram 2003-09-19 10:30 #92 Rev.: 1891

- minor change

3 lines of code changed in 1 file:

• GDE/MOLPHY: pstree.c (+3 -3)

westram 2003-09-19 10:20 #91 Rev.: 1890

this is a generated files!

0 lines of code changed in 1 file:

• GDE/MOLPHY: prot_tml.h (del)

westram 2003-09-19 10:17 #90 Rev.: 1889

contains removed sources

0 lines of code changed in 1 file:

• GDE/MOLPHY: unused_molphy_sources.tgz (new)

westram 2003-09-19 10:11 #89 Rev.: 1887

- use calloc

3 lines of code changed in 1 file:

• GDE/MOLPHY: protml.c (+3 -3)

westram 2003-09-19 10:11 #88 Rev.: 1886

- added mo_assert

3 lines of code changed in 1 file:

• GDE/MOLPHY: protml.h (+3)

westram 2003-09-19 10:08 #87 Rev.: 1885

missing parameter type

12 lines of code changed in 2 files:

• GDE/MOLPHY: mltree.c (+10 -10), njtree.c (+2 -1)

westram 2003-09-19 10:06 #86 Rev.: 1884

const fix

7 lines of code changed in 3 files:

• GDE/MOLPHY: getseq.c (+4 -4), matrixut.c (+1 -1), matrixut.h (+2 -2)

westram 2003-09-18 15:15 #85 Rev.: 1883

*** empty log message ***

48 lines of code changed in 3 files:

• PROBE_WEB: Makefile (new 29)
• PROBE_WEB/CLIENT: HttpSubsystem.java (+2 -2), TreeReader.java (+17 -11)

westram 2003-09-18 15:09 #84 Rev.: 1882

allow "plength=all" (faked)

1 lines of code changed in 1 file:

• PROBE_WEB/SERVER: getProbes.cgi (+1)

westram 2003-09-18 15:08 #83 Rev.: 1881

renamed files

22 lines of code changed in 2 files:

• PROBE_SERVER: update_probe_server_databases.sh (new 1)
• PROBE_WEB/SERVER: getVersion.cgi (new 21)

westram 2003-09-18 15:04 #82 Rev.: 1880

updated

1 lines of code changed in 1 file:

• ARBDB: ad_t_prot.h (+1)

westram 2003-09-18 15:04 #81 Rev.: 1879

- added GBT_read_plain_tree

48 lines of code changed in 1 file:

• ARBDB: adtools.c (+48 -26)

westram 2003-09-18 15:03 #80 Rev.: 1878

- added target pclt (probe java client)
- changed targets:
. ps=probe_server (was probe_set)
. pc=probe_client
. pst=probe_set
- allow arbxtras to fail

37 lines of code changed in 1 file:

• Makefile (+37 -21)

westram 2003-09-18 14:42 #79 Rev.: 1877

minor changes

82 lines of code changed in 4 files:

• PROBE_WEB/CLIENT: NodeError.java (+2 -2), ProbesGUIActionListener.java (+24 -28), TreeDisplay.java (+55 -63), WindowClosingAdapter.java (+1 -1)

westram 2003-09-18 14:41 #78 Rev.: 1876

- improved error handling

53 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeReader.java (+53 -7)

westram 2003-09-18 14:41 #77 Rev.: 1875

- added verbose flag

49 lines of code changed in 2 files:

• PROBE_WEB/CLIENT: TreeNode.java (+8 -4), TreeParser.java (+41 -43)

westram 2003-09-18 14:41 #76 Rev.: 1874

- Global available variables and functions (mostly for error handling)

11 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: Toolkit.java (new 11)

westram 2003-09-18 14:40 #75 Rev.: 1873

- makes HTTP errors readable
- error handling

106 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: ServerAnswer.java (+106 -47)

westram 2003-09-18 14:40 #74 Rev.: 1872

- pass title from client

7 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: ProbesGUI.java (+7 -9)

westram 2003-09-18 14:40 #73 Rev.: 1871

- basic dependencies added
- changes to call it from main ARB Makefile

68 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: Makefile (+68 -9)

westram 2003-09-18 14:40 #72 Rev.: 1870

- isInside() is more tolerant

3 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: LineArea.java (+3 -9)

westram 2003-09-18 14:40 #71 Rev.: 1869

- stores needed version (client/tree)
- does not load tree
- conductRequest reports error

124 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: HttpSubsystem.java (+124 -120)

westram 2003-09-18 14:39 #70 Rev.: 1868

- define known options by argument
- command line help
- check whether options are legal

69 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: CommandLine.java (+69 -37)

westram 2003-09-18 14:39 #69 Rev.: 1867

- added readTree
- improved error handling

68 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: Client.java (+68 -61)

huberj 2003-09-17 16:59 #68 Rev.: 1866

*** empty log message ***

3 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.cxx (+2 -3), SQ_main.cxx (+1 -1)

huberj 2003-09-17 16:31 #67 Rev.: 1865

*** empty log message ***

8 lines of code changed in 1 file:

• lib/pictures: seq_quality.fig (+8 -4)

westram 2003-09-17 14:53 #66 Rev.: 1864

return a random probe type (until probe types are implemented)

3 lines of code changed in 1 file:

• PROBE_SERVER/WORKER: psw_main.cxx (+3 -2)

westram 2003-09-17 14:27 #65 Rev.: 1863

returns needed client version

3 lines of code changed in 1 file:

• PROBE_WEB/SERVER: getTreeVersion.cgi (+3 -1)

westram 2003-09-17 14:24 #64 Rev.: 1862

ralf + lothar

155 lines of code changed in 6 files:

• PROBE_WEB/CLIENT: .cvsignore (new 5), Client.java (+33 -17), HttpSubsystem.java (+35 -26), Makefile (+2 -2), ServerAnswer.java (new 75), TreeReader.java (+5 -3)

westram 2003-09-17 14:20 #63 Rev.: 1861

changed syntax of probe-group-id

11 lines of code changed in 1 file:

• PROBE_SERVER/WORKER: psw_main.cxx (+11 -6)

richter 2003-09-17 11:10 #62 Rev.: 1860

Command line parser added, handover before holiday

109 lines of code changed in 3 files:

• PROBE_WEB/CLIENT: Client.java (+2 -2), CommandLine.java (new 105), HttpSubsystem.java (+2 -2)

westram 2003-09-17 09:59 #61 Rev.: 1859

deps updated

4 lines of code changed in 2 files:

• PROBE_SERVER/PROBE_GROUP_DESIGN: Makefile (+1 -1)
• PROBE_SERVER/WORKER: Makefile (+3 -1)

westram 2003-09-17 09:59 #60 Rev.: 1858

prepared to use mapping

2 lines of code changed in 1 file:

• PROBE_SERVER/WORKER: psw_main.cxx (+2 -1)

westram 2003-09-17 09:59 #59 Rev.: 1857

- command line options to optionally store/extend treefile
(not implemented yet)

24 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP_DESIGN: pgd_main.cxx (+24 -8)

westram 2003-09-17 09:57 #58 Rev.: 1856

- provides code to use existing species_mapping

70 lines of code changed in 1 file:

• PROBE_SERVER: mapping.h (new 70)

westram 2003-09-17 09:56 #57 Rev.: 1855

- transfers species_mapping to destination db
- saves mapped tree into destination db

27 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP: pg_main.cxx (+27)

westram 2003-09-17 09:55 #56 Rev.: 1854

- added PG_transfer_root_string_field

44 lines of code changed in 2 files:

• PROBE_SERVER/PROBE_GROUP: pg_db.cxx (+42 -4), pg_db.hxx (+2 -1)

westram 2003-09-17 09:55 #55 Rev.: 1853

updated

3 lines of code changed in 2 files:

• ARBDB: ad_t_lpro.h (+1), ad_t_prot.h (+2)

westram 2003-09-17 09:54 #54 Rev.: 1852

- added GBT_unlink_tree
- added GBT_write_plain_tree

60 lines of code changed in 1 file:

• ARBDB: adtools.c (+60 -30)

westram 2003-09-16 19:58 #53 Rev.: 1851

path fixes

1 lines of code changed in 1 file:

• PROBE_WEB/SERVER: probe_server.pm (+1 -2)

westram 2003-09-16 19:55 #52 Rev.: 1850

- tree group names where not saved in Newick-Format

2 lines of code changed in 1 file:

• AWT: AWT_imp_exp.cxx (+2 -2)

westram 2003-09-16 19:54 #51 Rev.: 1849

minor changes

9 lines of code changed in 1 file:

• PROBE_SERVER/WORKER: psw_main.cxx (+9 -4)

westram 2003-09-16 19:53 #50 Rev.: 1848

using functions from .pm

4 lines of code changed in 2 files:

• PROBE_WEB/SERVER: getMembers.cgi (+2 -7), getProbes.cgi (+2 -6)

westram 2003-09-16 19:53 #49 Rev.: 1847

- added treefilename, print_special_header, error functions
- added request/result file name generation
- safer operation by creating request with a different
name and renaming it after the file was completely generated.

54 lines of code changed in 1 file:

• PROBE_WEB/SERVER: probe_server.pm (+54 -5)

westram 2003-09-16 19:52 #48 Rev.: 1846

- returns server status info

0 lines of code changed in 1 file:

• PROBE_WEB/SERVER: getStatus.cgi (new)

westram 2003-09-16 19:52 #47 Rev.: 1845

- returns the tree in gzipped format

16 lines of code changed in 1 file:

• PROBE_WEB/SERVER: getTree.cgi (new 16)

westram 2003-09-16 19:52 #46 Rev.: 1844

- returns the tree version

13 lines of code changed in 1 file:

• PROBE_WEB/SERVER: getTreeVersion.cgi (+13 -8)

westram 2003-09-16 15:34 #45 Rev.: 1843

- uses write_std_request

8 lines of code changed in 2 files:

• PROBE_WEB/SERVER: getMembers.cgi (+4 -12), getProbes.cgi (+4 -12)

westram 2003-09-16 15:34 #44 Rev.: 1842

- added write_std_request

16 lines of code changed in 1 file:

• PROBE_WEB/SERVER: probe_server.pm (+16 -3)

westram 2003-09-16 15:34 #43 Rev.: 1841

- implemented encodePath
- 'getprobes' handles encoded and decoded paths
- added debug_.. results strings

88 lines of code changed in 1 file:

• PROBE_SERVER/WORKER: psw_main.cxx (+88 -27)

westram 2003-09-16 14:07 #42 Rev.: 1840

- added wait_answer() and send_result()
- handle empty result files

23 lines of code changed in 1 file:

• PROBE_WEB/SERVER: probe_server.pm (+23 -3)

westram 2003-09-16 14:07 #41 Rev.: 1839

- uses wait_answer() and send_result()

3 lines of code changed in 1 file:

• PROBE_WEB/SERVER: getProbes.cgi (+3 -7)

westram 2003-09-16 14:07 #40 Rev.: 1838

- returns list of probe-group members
- uses wait_answer() and send_result()

39 lines of code changed in 1 file:

• PROBE_WEB/SERVER: getMembers.cgi (new 39)

westram 2003-09-16 14:07 #39 Rev.: 1837

- returns a probe-group-id for each probe
- returns found=0 for unknown inner nodes
- new command 'getmembers'

88 lines of code changed in 1 file:

• PROBE_SERVER/WORKER: psw_main.cxx (+88 -25)

westram 2003-09-16 14:06 #38 Rev.: 1836

- uses -f for remove

1 lines of code changed in 1 file:

• PROBE_SERVER: restart_all_servers.sh (+1 -1)

westram 2003-09-16 14:06 #37 Rev.: 1835

*** empty log message ***

4 lines of code changed in 1 file:

• arb_CHANGES.txt (+4)

westram 2003-09-16 12:25 #36 Rev.: 1834

- call SQ_reset_quality_calcstate

5 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+5 -2)

westram 2003-09-16 12:25 #35 Rev.: 1833

- added copyright and prototype for SQ_reset_quality_calcstate

21 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.h (+21)

westram 2003-09-16 12:24 #34 Rev.: 1832

- added SQ_reset_quality_calcstate

35 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+35 -4)

huberj 2003-09-15 16:12 #33 Rev.: 1831

*** empty log message ***

45 lines of code changed in 4 files:

• SEQ_QUALITY: SQ_consensus_marked.h (+6), SQ_functions.cxx (+21 -15), SQ_functions.h (+1 -1), SQ_main.cxx (+17 -6)

westram 2003-09-15 12:46 #32 Rev.: 1830

path to workerdir fixed to work on trance webserver

2 lines of code changed in 1 file:

• PROBE_WEB/SERVER: probe_server.pm (+2 -1)

westram 2003-09-15 12:03 #31 Rev.: 1829

added WORKER

14 lines of code changed in 1 file:

• PROBE_SERVER: Makefile (+14 -6)

westram 2003-09-15 12:03 #30 Rev.: 1828

scripts to update/start/stop servers

80 lines of code changed in 4 files:

• PROBE_SERVER: kill_all_servers.sh (new 28), restart_all_servers.sh (new 9), start_all_servers.sh (new 20), update_probe_server.sh (+23 -10)

westram 2003-09-15 12:02 #29 Rev.: 1827

common code for all probe_server processes

122 lines of code changed in 1 file:

• PROBE_SERVER: common.h (new 122)

westram 2003-09-15 12:01 #28 Rev.: 1826

added pt-server for probe_server (should be hidden in ARB)

12 lines of code changed in 1 file:

• lib: arb_tcp.dat (+12 -12)

westram 2003-09-15 12:00 #27 Rev.: 1825

dependencies updated

2 lines of code changed in 2 files:

• PROBE_SERVER/PROBE_GROUP: Makefile (+1 -1)
• PROBE_SERVER/PROBE_GROUP_DESIGN: Makefile (+1)

westram 2003-09-15 12:00 #26 Rev.: 1824

added information about database type and state

51 lines of code changed in 2 files:

• PROBE_SERVER/PROBE_GROUP: pg_main.cxx (+34 -21)
• PROBE_SERVER/PROBE_GROUP_DESIGN: pgd_main.cxx (+17 -5)

westram 2003-09-15 11:58 #25 Rev.: 1823

link to PROBE_WEB/SERVER in PROBE_SERVER

5 lines of code changed in 1 file:

• SOURCE_TOOLS: generate_all_links.sh (+5)

westram 2003-09-15 11:57 #24 Rev.: 1822

ask for probes of a specific node

31 lines of code changed in 1 file:

• PROBE_WEB/SERVER: getProbes.cgi (+31 -38)

westram 2003-09-15 11:56 #23 Rev.: 1821

*** empty log message ***

46 lines of code changed in 2 files:

• PROBE_WEB/SERVER: probe_server.pm (new 46), test_getProbes.cgi (new)

westram 2003-09-15 11:55 #22 Rev.: 1820

comment about sensibility of encode routine

19 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeNode.java (+19 -15)

westram 2003-09-15 11:54 #21 Rev.: 1819

initial version of probe-server worker process

588 lines of code changed in 3 files:

• PROBE_SERVER/WORKER: Makefile (new 2), README (new 22), psw_main.cxx (new 564)

yadhu 2003-09-12 13:45 #20 Rev.: 1818

To import xml format trees in to ARB Database.

379 lines of code changed in 6 files:

• XML_IMPORT: Makefile (new 51)
• XML_IMPORT/IMP_TREE: Makefile (new 30), MySAXHandler.cxx (new 139), MySAXHandler.hxx (new 45), testParser.cxx (new 83), testParser.hxx (new 31)

westram 2003-09-12 12:27 #19 Rev.: 1817

minor changes

183 lines of code changed in 5 files:

• PROBE_SERVER/PROBE_GROUP: pg_db.hxx (+1 -1), pg_def.hxx (+1 -1), pg_main.cxx (+2 -2), pg_search.cxx (+92 -92)
• PROBE_SERVER/PROBE_GROUP_DESIGN: pgd_main.cxx (+87 -15)

westram 2003-09-12 12:26 #18 Rev.: 1816

* CHIP/ca_probe.hxx: - changed some prefixes
* CHIP/ca_probe.cxx: - changed some prefixes
- fixed undefined code in parse_match_info (returned address of local variable)

39 lines of code changed in 2 files:

• CHIP: ca_probe.cxx (+33 -34), ca_probe.hxx (+6 -6)

westram 2003-09-12 10:51 #17 Rev.: 1815

new makefiles

136 lines of code changed in 3 files:

• PROBE_SERVER: Makefile (new 70)
• PROBE_SERVER/PROBE_GROUP: Makefile (new 62)
• PROBE_SERVER/PROBE_GROUP_DESIGN: Makefile (new 4)

westram 2003-09-12 10:50 #16 Rev.: 1814

tinas code

860 lines of code changed in 5 files:

• PROBE_SERVER/PROBE_GROUP: pg_db.cxx (new 266), pg_db.hxx (new 70), pg_def.hxx (new 1), pg_search.cxx (new 485), pg_search.hxx (new 38)

westram 2003-09-12 10:50 #15 Rev.: 1813

- fixed CL option scanner
- fixed error handling

648 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP: pg_main.cxx (new 648)

westram 2003-09-12 10:50 #14 Rev.: 1812

- fixed error handling
- removed unused command line arguments
- initialize pt-server only once

486 lines of code changed in 1 file:

• PROBE_SERVER/PROBE_GROUP_DESIGN: pgd_main.cxx (new 486)

westram 2003-09-12 10:49 #13 Rev.: 1811

shell script to build probe server databases

10 lines of code changed in 1 file:

• PROBE_SERVER: update_probe_server.sh (new 10)

westram 2003-09-12 10:49 #12 Rev.: 1810

- global definitions for PROBE_GROUP and PROBE_GROUP_DESIGN

33 lines of code changed in 1 file:

• PROBE_SERVER: global_defs.h (new 33)

westram 2003-09-12 10:39 #11 Rev.: 1809

- removed calls to PROBE_GROUP and PROBE_GROUP_DESIGN
- added call to PROBE_SERVER

6 lines of code changed in 1 file:

• Makefile (+6 -27)

westram 2003-09-12 10:32 #10 Rev.: 1808

- updated dependencies

7 lines of code changed in 2 files:

• EDIT4: Makefile (+6)
• SEQ_QUALITY: Makefile (+1 -2)

westram 2003-09-11 18:10 #9 Rev.: 1807

*** empty log message ***

879 lines of code changed in 2 files:

• ARBDB: arbdb.h (+1 -1)
• EDIT4: ED4_protein_2nd_structure.cxx (+878 -871)

westram 2003-09-11 18:09 #8 Rev.: 1806

prototype II

92 lines of code changed in 5 files:

• EDIT4: ED4_main.cxx (+37 -3), ED4_text_terminals.cxx (+45 -13), ed4_class.hxx (+2), ed4_protein_2nd_structure.h (del), ed4_protein_2nd_structure.hxx (new 8)

richter 2003-09-11 16:13 #7 Rev.: 1805

Changed downliad behaviour, zipped treefile placed outside of jar-file
Tree version control and tree version handling nearly complete and implemented

261 lines of code changed in 10 files:

• PROBE_WEB/CLIENT: Client.java (+33 -5), HttpSubsystem.java (+146 -10), Makefile (+2 -1), ProbeMenu.java (+5 -1), ProbesGUI.java (+3 -2), ProbesGUIActionListener.java (+4 -1), TreeDisplay.java (+39 -2), TreeNode.java (+4 -2), TreeReader.java (+24 -6), demo.newick (+1 -1)

urban 2003-09-11 15:47 #6 Rev.: 1804

prototype

1160 lines of code changed in 4 files:

• EDIT4: ED4_protein_2nd_structure.cxx (new 1120), ED4_text_terminals.cxx (+28), Makefile (+2 -1), ed4_protein_2nd_structure.h (new 10)

huberj 2003-09-11 15:46 #5 Rev.: 1803

*** empty log message ***

100 lines of code changed in 6 files:

• SEQ_QUALITY: Makefile (+1), SQ_consensus_marked.cxx (del), SQ_consensus_marked.h (new 55), SQ_consensus_marked.hxx (del), SQ_functions.cxx (+36 -4), SQ_main.cxx (+8 -7)

richter 2003-09-10 13:41 #4 Rev.: 1802

improved version of dsmzconnect.pl with automatic browser invocation

4 lines of code changed in 1 file:

• SH: dszmconnect.pl (+4 -1)

richter 2003-09-10 12:54 #3 Rev.: 1801

special perl script to connect (valid) names with DSMZ taxonomic database
via normal hyperlink mechanism used in ARB

111 lines of code changed in 1 file:

• SH: dszmconnect.pl (new 111)

huberj 2003-09-01 17:53 #2 Rev.: 1800

*** empty log message ***

26 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_consensus_marked.cxx (new 13), SQ_consensus_marked.hxx (new 13)

huberj 2003-09-01 17:51 #1 Rev.: 1799

still problems

12 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.cxx (+8 -3), SQ_main.cxx (+4 -4)

August 2003 »